RT-qPCR analysis of micro-dissected material from stained FFPET section

ABSTRACT

The present invention refers to a method for immuno-histochemical staining of a formalin-fixed, paraffin-embedded tissue section comprising the steps of a) providing a solid support, b) mounting the formalin-fixed, paraffin-embedded tissue section onto the solid support, c) removing the paraffin from the formalin-fixed, paraffin-embedded tissue section, d) heating the tissue section mounted on the solid support to retrieve epitopes at 50 to 70° C. for 12 to 24 h, and e) staining the tissue section mounted on the solid support, wherein at least step e) is performed in the presence of 0.5 to 3.0 M sodium chloride. The present invention further refers to a kit for performing the method.

BACKGROUND OF THE INVENTION

The present description refers to a method for immuno-histochemicalstaining of a formalin-fixed, paraffin-embedded tissue sectioncomprising the steps of a) providing a solid support, b) mounting theformalin-fixed, paraffin-embedded tissue section onto the solid support,c) removing the paraffin from the formalin-fixed, paraffin-embeddedtissue section, d) heating the tissue section mounted on the solidsupport to retrieve epitopes at 50 to 70° C. for 12 to 24 h, and e)staining the tissue section mounted on the solid support, wherein atleast step e) is performed in the presence of 0.5 to 3.0 M sodiumchloride. The present description further refers to a kit for performingthe method.

Formalin fixation and paraffin embedding (FFPE) is a well-knownprocedure for tissue fixation for diagnostic histology and long termstorage in clinical routine. Large archives of FFPE tissue (FFPET)samples are used for biomarker discovery studies as well as earlyclinical studies. Furthermore, FFPET samples can be used for isolationof RNA which can further be applied in gene expression analyses.Although, RNA from FFPET samples shows a high degree of degradation, itis still sufficient for RT-qPCR analyses provided that a sufficientamount of material is used for RNA isolation. Such analyses can be usedto generate a first biomarker hypothesis and simply for hypothesistesting (Lohmann et al, Methods. 2013 January; 59(1)).

To be able to separate blood vessels and tumor cell nests from FFPEtissue sections and perform RT-qPCR analysis, we combined the followingtechnologies: laser capture micro-dissection (LCM) from FFPET afterimmuno-histochemical staining with RT-qPCR analysis afterpre-amplification of the cDNA.

The challenges the skilled person is faced with when combining LCM fromIHC-stained FFPET sections followed by RT-qPCR analysis is the verylimited amount of material after LCM, RNA degradation after fixation ofthe sample tissue and in addition the RNA degradation during theimmuno-histological staining procedure. The classical staining procedureincludes epitope retrieval (e.g. HIER protocol at 98° C.) and incubationtimes with buffers that cannot be produced under RNAse free conditions(antibody solution, washing buffers, dyes). The described RNAdegradation in combination with the very limited amount of materialafter LCM is the major problem of this workflow if the RNA is intendedto be used in RT-qPCR analyses. The degradation of RNA lead tounreliable results in gene expression analyses following LCM, e.g. theratio between a biomarker of interest and a reference gene. mRNAstability is gene-specific and therefore they are degrading to adifferent extend, leading to wrong results in relative quantificationfor gene expression analysis.

To overcome this problem of RNA degradation, different procedures havebeen established to keep the degradation to a minimum. The majority ofpublications for example use Fresh Frozen (FF) tissue which has theadvantage of less degradation processes when used for RT-qPCR analyses.The major drawback, however, is the fact that FF tissue is a largelylimited source as compared to FFPET (Buckanovich et al., Cancer BiolTher. 2006 June; 5(6):635-42; Gjerdrum et al., Diagn Mol Pathol 2004(13), p. 224-233) It is often difficult to obtain a sufficient amount ofFF tissue for performing a study leading to statistically significantresults. Furthermore the clinical sample material available forretrospective testing is typically FFPET.

Therefore, a main focus in this field was the development of techniquesusing FFPET in combination with LCM and RT-qPCR analyses minimizing theRNA degradation. Ultra-fast staining procedures for FFPET-sections weredeveloped to minimize RNA degradation during the staining. However,analyzing the RNA from such micro-dissected, ultra-fast stainedFFPET-sections showed that after antibody incubation with very shortincubation periods (2×5 min) still approximately 90% of the RNA wasdegraded as compared to a simple histological stain (Hematoxylin)(Gjerdrum et al., Diagn Mol Pathol 2004 (13)). In addition, ultra-faststaining protocols are not applicable to all antibodies as some needseveral hours to overnight incubation (Brown et al., RNA Journal 2009(15), p. 2364-2374). Such long term incubation procedures lead tomassive RNA degradation, such that gene expression analyses are simplyimpossible.

Therefore, the object of the present description is to provide animproved staining technique for FFPET-sections subsequently used for RNAisolation, wherein the improved staining technique leads to a yield andquality of the isolated RNA from FFPET-sections sufficient for RNAanalyses, such as gene expression analyses.

SUMMARY OF THE INVENTION

It was found that high salt concentrations of 0.5 to 3.0 M sodiumchloride in the staining method described herein applied to tissuesections mounted on the solid support prevent degradation of RNAisolated subsequently from the tissue sections. The method according tothe description is suitable for staining procedures, where RNA isisolated after the staining and where high quality RNA is required, suchas for gene expression analyses.

The present description thus refers to a method for immuno-histochemicalstaining of a formalin-fixed, paraffin-embedded tissue sectioncomprising the steps of a) providing a solid support, b) mounting theformalin-fixed, paraffin-embedded tissue section onto the solid support,c) removing the paraffin from the formalin-fixed, paraffin-embeddedtissue section, d) heating the tissue section mounted on the solidsupport to retrieve epitopes at 50 to 70° C. for 12 to 24 h, and e)staining the tissue section mounted on the solid support, wherein atleast step e) is performed in the presence of 0.5 to 3.0 M sodiumchloride.

Furthermore, the present description refers to a kit for performing themethod as described herein, wherein the kit comprises a) a solid supportcoated with poly-lysine, b) a solution for epitope retrieval, and c) asolution for immuno-histochemical staining comprising sodium chloride ina concentration of 0.5 to 3.0 M.

FIGURES

FIG. 1: The figure shows the result of a spectral photometricconcentration analysis of isolated RNA. Depicted is the median+/−standard deviation of the RNA-concentrations from extracts isolated fromunstained FFPET sections (not stained), isolated from FFPET sectionsstained with CD31 in the absence of sodium chloride (without NaCl) andisolated from FFPET sections stained with CD31 in the presence of sodiumchloride (with NaCl). Data were obtained from three independentreplicates each.

FIG. 2: The figure shows the Cp-values of an RT-qPCR analysis of thereference gene HPRT (hypoxanthine-guanine phosphoribosyltransferase).Depicted is the median+/− standard deviation of the Cp-values fromRT-qPCR experiments. RNA was isolated from unstained FFPET sections (notstained), isolated from FFPET sections stained with CD31 in the absenceof sodium chloride (without NaCl) and isolated from FFPET sectionsstained with CD31 in the presence of sodium chloride (with NaCl). Datawere obtained from three independent replicates each.

FIG. 3: The figure shows the Cp-values of an RT-qPCR analysis of thereference gene ALAS1 (delta-aminolevulinate synthase 1). Depicted is themedian+/− standard deviation of the Cp-values from RT-qPCR experiments.RNA was isolated from unstained FFPET sections (not stained), isolatedfrom FFPET sections stained with CD31 in the absence of sodium chloride(without NaCl) and isolated from FFPET sections stained with CD31 in thepresence of sodium chloride (with NaCl). Data were obtained from threeindependent replicates each.

FIG. 4: The figure shows the expression of Marker 1 and Marker 2normalized to the reference gene HPRT, respectively. Depicted is therelative gene expression of Marker 1 and Marker 2 from microdissectedtumor cells and vessel cells, respectively. Experiments were performedin duplicates.

DETAILED DESCRIPTION OF THE INVENTION

The following definitions are set forth to illustrate and define themeaning and scope of various terms used herein.

The terms “a”, “an” and “the” generally include plural referents, unlessthe context clearly indicates otherwise.

The term “about” as used herein in conjunction with a numerical valuemodifies that value by extending the boundaries above and below thevalues. In general, the term “about” modifies a numerical value aboveand below the stated value by a variance of 5% higher or lower. Forexample a value of “about 100” means a range of “95 to 105”.

The term “amplification” generally refers to the production of aplurality of nucleic acid molecules from a target nucleic acid whereinprimers hybridize to specific sites on the target nucleic acid moleculesin order to provide an initiation site for extension by a polymerase.Amplification can be carried out by any method generally known in theart, such as but not limited to: standard PCR, long PCR, hot start PCR,qPCR, RT-PCR and Isothermal Amplification.

The term “antibody” as used herein refers to a complete immunoglobulin,such as an IgA, IgD, IgE, IgG or IgM or to a fragment of an antibody,such as a Fab, Fv or Fc or a fused antibody, a fused antibody fragmentor any other derivative of an antibody. The term “labeled antibody”refers to an antibody that is labeled with an enzyme, a fluorescent dye,a chemiluminescent substance, biotin, avidin or a radioisotope.

The term “epitope” refers to an antigenic region of a compound, such asa protein, a carbohydrate or a lipid. The antigenic region typicallyconsists of 5 to 8 amino acids. The epitope is specifically recognizedby the antigen binding sites of the respective antibody.

The term “fixed tissue or cell” is used herein as known to the expertskilled in the art and refers to biological tissue or cells which arepreserved from decay by chemical fixation methods. Such methods preventautolysis or putrefaction within such biological tissue or cells.Fixation terminates biochemical reactions and increases the mechanicalstability of the treated tissue.

The term “immuno-histochemistry” and “immuno-histochemical” refers to atechnique for detecting the presence of an antigen with an antibodycapable of specifically binding to said antigen in histological samples.The detection of the antibody-antigen complex occurs usually by achromogenic reaction with an enzyme-labeled antibody or by a fluorescentlabeled antibody.

The term “macrodissection” as used herein refers to the process ofscratching an area of interest from a tissue section mounted on a solidsupport, such as a microscope slide, by using a tool such as a scalpelor a spatula.

The term “membrane slide” as used herein refers to solid supports ormicroscope slides for use in Laser Capture Microdissection (LCM). Formicrodissection glass slides covered with a membrane or frame slidesthat consist of a metal frame which can be covered with variousmembranes can be used. The material of the membrane can be selected fromthe group consisting of polyphenylene sulfide (PPS), polyethylenenaphthalate (PEN), polyester (POL) and fluocarbon (FLUO).

The term “microdissection” as used herein refers to the process ofcutting and separating one or more specific cells or an area of interestfrom a tissue sample. Microdissection can for example be performed usinglaser capture microdissection (LCM) by cutting the relevant area with alaser.

The term “nucleic acid” generally refers to DNA or RNA, whether it is aproduct of amplification, synthetically created, products of reversetranscription of RNA or naturally occurring. Typically, nucleic acidsare single- or double-stranded molecules and are composed of naturallyoccurring nucleotides. Double-stranded nucleic acid molecules can have3′ or 5′ overhangs and as such are not required or assumed to becompletely double-stranded over their entire length. Furthermore, theterm nucleic acid can be composed of non-naturally occurring nucleotidesand/or modifications to naturally occurring nucleotides. Examples arelisted herein, but are not limited to: phosphorylation of 5′ or 3′nucleotides to allow for ligation or prevention of exonucleasedegradation/polymerase extension, respectively; amino, thiol, alkyne, orbiotinyl modifications for covalent and near covalent attachments;fluorophores and quenchers; phosphorothioate, methylphosphonates,phosphoroamidates and phosphorotiester linkages between nucleotides toprevent degradation; methylation; and modified bases such asdeoxyInosine, 5-Bromo dU, deoxyUridine, 2-Aminopurine, dideoxyCytidine,5-Methyl dC, locked nucleic acids (LNA's), Iso-dC and -dG bases,2′-O-Methyl RNA bases and Fluorine Modified Bases.

The term “poly-lysine” refers to a molecule that contains up to severalhundreds of repeating units and is suitable for increasing the affinitybetween a sample, such as a tissue section, and the membrane side ontowhich the sample is mounted. A poly-lysine according to the descriptionis poly-L-lysine. Poly-L-lysine according to the description has amolecular weight from 70 to 300 kDa. Poly-L-lysine can be digested byproteases. Another poly-lysine according to the description is forexample poly-D-lysine. Poly-D-lysine according to the description has amolecular weight from 70 to 300 kDa. Poly-D-lysine is resistant toprotease digestion.

The term “qPCR” generally refers to the PCR technique known as real-timequantitative polymerase chain reaction, quantitative polymerase chainreaction or kinetic polymerase chain reaction. This techniquesimultaneously amplifies and quantifies target nucleic acids using PCRwherein the quantification is by virtue of an intercalating fluorescentdye or sequence-specific probes which contain fluorescent reportermolecules that are only detectable once hybridized to a target nucleicacid.

The term “RNA” is used herein as known to the expert skilled in the artand refers to pre-mRNA, pre-mRNA transcripts, mRNA, transcriptprocessing intermediates, mature mRNA used for translation andtranscripts from a gene or genes, or nucleic acids derived therefrom.Transcript processing includes processes such as splicing, editing,modifying and degrading. mRNA including samples include, but are notlimited to mRNA, mRNA transcripts of the gene or genes, cDNA originatingfrom mRNA using reverse transcription, RNA transcribed from amplifiedDNA, cRNA transcribed from cDNA, DNA amplified from the genes, and thelike.

The term “solid support” is used herein as known to the expert skilledin the art and refers to any solid material, having a surface area towhich tissue sections can be mounted or attached. The support can be acombination of materials such as plastic on glass, carbon on glass, andthe like. In a specific embodiment, the solid support can be a “membraneslide” as defined above.

The present description refers to a method for immuno-histochemicalstaining of a formalin-fixed, paraffin-embedded tissue sectioncomprising the steps of a) providing a solid support, b) mounting theformalin-fixed, paraffin-embedded tissue section onto the solid support,c) removing the paraffin from the formalin-fixed, paraffin-embeddedtissue section, d) heating the tissue section mounted on the solidsupport to retrieve epitopes at 50 to 70° C. for 12 to 24 h, and e)staining the tissue section mounted on the solid support, wherein atleast step e) is performed in the presence of 0.5 to 3.0 M sodiumchloride. As known by the skilled person, the term “sodium chloride” andempirical formula “NaCl” can be used interchangeably within the presentdescription. In one embodiment, the sodium chloride is present in aconcentration of 1.5 to 2.5 M. In a more specific embodiment, the sodiumchloride is present in a concentration of about 1.8 to 2.2 M. In an evenmore specific embodiment, the sodium chloride is present in aconcentration of about 2 M.

It was found that, as can be taken also from the Examples, using highsalt concentrations of 0.5 to 3.0 M sodium chloride in at least the stepof staining the tissue section mounted on the solid support, prevent RNAisolated subsequently from the FFPET section from degradation. Thus, themethod according to the description using high salt concentrations of0.5 to 3.0 M sodium chloride is suitable for staining procedures, whereRNA is isolated after the staining and where high quality RNA isrequired, such as for RT-qPCR experiments.

In one embodiment, the method further comprises the steps of f)dissecting from the stained tissue section mounted on the solid supportan area of interest, g) isolating RNA from the area of interest, h)analyzing the isolated RNA. In one embodiment, analyzing the isolatedRNA comprises any method known in the art, such as RNA profiling, RNAsequencing and gene expression analyses. Thus, the method according tothe description can be used to isolate RNA with increased quality fromFFPET section such that the results of basically any subsequent methodcan be improved significantly by applying the RNA stabilization in FFPETsections as described herein.

In another embodiment, the method further comprises the steps of f)dissecting from the stained tissue section mounted on the solid supportan area of interest, g) isolating RNA from the area of interest, h)reverse transcribing the isolated RNA into cDNA, i) amplifying andquantifying the cDNA. In one embodiment, steps h) and i) are performedas one-step PCR. In another embodiment, steps h) and i) are performed astwo-step PCR. In a specific embodiment, the step of amplifying andquantifying the cDNA is performed by Real Time PCR.

In one embodiment, the solid support is coated with poly-L-lysine. Inanother embodiment, the solid support is coated with poly-D-lysine. In aspecific embodiment, the solid support is coated with poly-L-lysine orpoly-D-lysine by applying a solution of poly-L-lysine or poly-D-lysineto the solid support. In one embodiment, the solid support is incubated15 to 45 min after the application of the solution of poly-L-lysine orpoly-D-lysine. In a specific embodiment, the solid support is incubated30 min after the application of the solution of poly-L-lysine orpoly-D-lysine. In a specific embodiment, the solution has aconcentration of 0.05 to 2% of poly-L-lysine or poly-D-lysine. In a morespecific embodiment, the solution has a concentration of 0.1% ofpoly-L-lysine or poly-D-lysine. In another specific embodiment, thepoly-L-lysine or poly-D-lysine has a molecular weight from 70 to 300kDa. In another specific embodiment, the solid support is a membraneslide.

In one embodiment, the solid support is treated with3-aminopropyltriethoxysilane (APES). Such silanization can be performedto functionalize the surface of the solid support with alkoxysilanemolecules resulting in an increased attachment of the tissue sections onthe solid support.

In one embodiment, the formalin-fixed, paraffin-embedded tissue sectionmounted on the solid support has a thickness of 2 to 10 μm. In aspecific embodiment, the formalin-fixed, paraffin-embedded tissuesection mounted on the solid support has a thickness of 4 to 6 μm. In amore specific embodiment, the formalin-fixed, paraffin-embedded tissuesection mounted on the solid support has a thickness of about 5 μm.

In one embodiment, removing the paraffin is performed by incubating thetissue section mounted on the solid support in xylol. Subsequently, thetissue section mounted on the solid support is rehydrated in a series ofdecreasing concentration of ethanol, e.g. several seconds in each of100%, 96% and 70% ethanol, followed by 2×1 min in water.

In order to maximally prevent the RNA from degradation, alow-temperature heat induced epitope retrieval (LT-HIER) protocol wasestablished. Epitope retrieval was found to provide the best results,when the tissue section mounted on the solid support was heated at 60°C. for 16 h at pH8. In one embodiment, sodium chloride can be present ina concentration of 2 M in the solution for epitope retrieval.

Thus, in one embodiment, heating of the tissue section mounted on thesolid support is performed in the presence of 0.5 to 3.0 M sodiumchloride. In a specific embodiment, heating of the tissue sectionmounted on the solid support is performed in the presence of 1.5 to 2.5M sodium chloride. In another specific embodiment, heating of the tissuesection mounted on the solid support is performed in the presence of 1.8to 2.2 M sodium chloride. In an even more specific embodiment, heatingof the tissue section mounted on the solid support is performed in thepresence of about 2.0 M sodium chloride.

In one embodiment, heating of the tissue section mounted on the solidsupport is performed at 50 to 70° C. In a specific embodiment, heatingof the tissue section mounted on the solid support is performed at 55 to65° C. In another specific embodiment, heating of the tissue sectionmounted on the solid support is performed at 58 to 62° C. In an evenmore specific embodiment, heating of the tissue section mounted on thesolid support is performed at about 60° C.

In one embodiment, heating of the tissue section mounted on the solidsupport is performed for 12 to 24 h. In a specific embodiment, heatingof the tissue section mounted on the solid support is performed for 14to 18 h. In a more specific embodiment, heating of the tissue sectionmounted on the solid support is performed for 15 to 17 h. In an evenmore specific embodiment, heating of the tissue section mounted on thesolid support is performed for about 16 h.

In one embodiment, heating of the tissue section mounted on the solidsupport is performed at pH 5 to 9. In a specific embodiment, heating ofthe tissue section mounted on the solid support is performed at pH 7.5to 8.5. In a more specific embodiment, heating of the tissue sectionmounted on solid support is performed at pH 7.8 to 8.2. In a specificembodiment, heating of the tissue section mounted on the solid supportis performed at a pH value of about 8.

In a specific embodiment, heating of the tissue section mounted on thesolid support is performed at about 60° C. for about 16 h at a pH valueof about 8. In one embodiment, sodium chloride can be present in aconcentration of 2 M in the solution for epitope retrieval.

After the heating step, the tissue section mounted on the solid supportis cooled in buffer with a concentration of 0.5 to 3.0 M sodiumchloride. In a specific embodiment, the buffer is TBS-T. In anotherspecific embodiment, sodium chloride is present in a concentration ofabout 2 M.

In one embodiment, the staining of the tissue section mounted on thesolid support comprises an antibody based staining. In a specificembodiment the antibody-based staining comprises the use of a primaryantibody and a secondary antibody. In a more specific embodiment, theprimary antibody is a CD31-binding antibody. In an even more specificembodiment, the primary antibody is CD31 monoclonal antibody (mAb) CloneJC70. In a specific embodiment the secondary antibody is an anti-mouseantibody. In a more specific embodiment, the secondary antibody iscovalently bound to an enzyme capable of transforming a substrate intoone or more products. In an even more specific embodiment, the secondaryantibody is covalently bound to horseradish peroxidase (HRP).

Antibody based staining was found to provide the best results, when thetissue section mounted on the solid support was incubated with theprimary antibody at 37° C. for 1 h, wherein sodium chloride was presentin a concentration of 2 M. In one embodiment, incubation of the tissuesection mounted on the solid support with the primary antibody isperformed at 34 to 40° C. In one embodiment, incubation of the tissuesection mounted on the solid support with the primary antibody isperformed for 0.5 to 1.5 h. In one embodiment, incubation of the tissuesection mounted on the solid support with the primary antibody isperformed in the presence of 0.5 to 3.0 M sodium chloride. In a specificembodiment, incubation of the tissue section mounted on the solidsupport with the primary antibody is performed at about 37° C. Inanother specific embodiment, incubation of the tissue section mounted onthe solid support with the primary antibody is performed for about 1 h.In yet another specific embodiment, incubation of the tissue sectionmounted on the solid support with the primary antibody is performed inthe presence of about 2.0 M sodium chloride. In a more specificembodiment, incubation of the tissue section mounted on the solidsupport with the primary antibody is performed at about 37° C. for about1 h, wherein sodium chloride is present in a concentration of about 2 M.

Incubation with the secondary antibody was performed at room temperaturefor 2 h in a humidity chamber, wherein sodium chloride was present in aconcentration of 2 M. In one embodiment, incubation of the tissuesection mounted on the solid support with the secondary antibody isperformed at 16 to 24° C. In one embodiment, incubation of the tissuesection mounted on the solid support with the secondary antibody isperformed for 1.5 to 2.5 h. In one embodiment, incubation of the tissuesection mounted on the solid support with the secondary antibody isperformed in the presence of 0.5 to 3.0 M sodium chloride. In a specificembodiment, incubation of the tissue section mounted on the solidsupport with the secondary antibody is performed at about 20° C. Inanother specific embodiment, incubation of the tissue section mounted onthe solid support with the secondary antibody is performed for about 2h. In yet another specific embodiment, incubation of the tissue sectionmounted on the solid support with the secondary antibody is performed inthe presence of about 2.0 M sodium chloride. In a more specificembodiment, incubation of the tissue section mounted on the solidsupport with the secondary antibody is performed at about 20° C. forabout 2 h, wherein sodium chloride is present in a concentration ofabout 2 M.

In one embodiment, the staining of the tissue section mounted on thesolid support further comprises an enzyme-substrate reaction catalyzedby an enzyme covalently bound to the secondary antibody. Thus, in aspecific embodiment, the staining comprises the use of a labeledantibody. The enzyme can be selected from the group consisting ofperoxidases and alkaline phosphatases. Peroxidases, such as HRP, arecapable of transforming substrates selected from the group consisting of3,3′-diaminobenzidin (DAB), 3-amino-9-ethylcarbazol (AEC),4-chlor-1-naphthol (CN) and p-phenylendiamin dihydrochloride. Alkalinephosphatases are capable of transforming substrates selected from thegroup consisting of naphthol as-mx-phosphate, hexazotizingtriamino-tritolyl-methanchloride, naphthol AS-BI-phosphate, naphtholAS-TR-phosphate, 5-brom-4-chlor-3-indoxylphosphat (BCIP),nitroblue-tetrazolium (NBT), iodnitrotetrazolium-violett (INT), Fast RedTR, Fast Red LB, Fast Blue BB and Fast Garnet GBC.

In a specific embodiment, the enzyme capable of transforming thesubstrate is HRP. In a specific embodiment, the substrate transformed byHRP is DAB. In one embodiment, the DAB staining is performed in thepresence of 0.5 to 3.0 M sodium chloride. In a specific embodiment,sodium chloride is present in a concentration of about 2 M. In oneembodiment, the DAB staining was performed for 5-20 min at roomtemperature. In a specific embodiment, the DAB staining was performedfor about 10 min at room temperature.

In one embodiment, the solid support is a membrane slide. In a specificembodiment, the solid support is a membrane slide suitable for LCM. In aspecific embodiment, the membrane slide is a polyethylene naphthalatemembrane slide. It has been shown that commercially available membraneslides, such as polyethylene naphthalate membrane slides are notsuitable for the method according to the present description. Thecommercially available membrane slides do not provide enough adhesion tothe FFPET sections during the step of heating the tissue sectionsmounted on the coated membrane slides to retrieve epitopes. In order toimprove the adhesion between the membrane slides and the FFPET sectionsduring the step of heating, the membrane slides were coated withpoly-L-lysine which increased the adhesion between the membrane slidesand the FFPET sections in a way that the FFPET sections were stablyattached to the membrane slides.

In one embodiment, the step of dissecting from the stained tissuesection mounted on the solid support an area of interest comprisesmicrodissecting or macrodissecting an area of interest. In a specificembodiment, the step of microdissecting comprises the process of cuttingand separating one or more specific cells or an area of interest from atissue sample. Microdissection can for example be performed using lasercapture microdissection (LCM) by cutting the relevant area with a laser.In a specific embodiment, the step of macrodissecting comprises theprocess of scratching an area of interest from a tissue section mountedon a solid support, such as a microscope slide, by using a tool such asa scalpel or a spatula.

In the method according to the description, LCM was used on the stainedFFPET section attached to the membrane slide to cut an area of interestfrom the tissue section. The area of interest was subsequently used forRNA isolation. In one embodiment, the area of interest has a size of0.5-5 mm². In a specific embodiment, the area of interest has a size of1-2 mm². RNA was isolated from the area of interest using methods wellknown in the art, such as by using the High Pure FFPET RNA IsolationKit® (Roche Diagnostics GmbH). The isolated RNA was subsequently reversetranscribed in order to obtain cDNA. Due to limited amount of cDNA andto provide sufficient nucleic acid for a qPCR experiment, apreamplification step can be performed on the cDNA prior toamplification by qPCR. Thus, in one embodiment, the method according tothe description further comprises the steps of f) microdissecting fromthe stained tissue section mounted on the coated membrane slide an areaof interest, g) isolating RNA from the area of interest, h) reversetranscribing the isolated RNA into cDNA, i) preamplifying the cDNA, andj) amplifying and quantifying the preamplified cDNA. In a specificembodiment, the step of amplifying and quantifying the preamplified cDNAis performed by Real Time PCR.

In a specific embodiment, the present description refers to a method forimmuno-histochemical staining of a formalin-fixed, paraffin-embeddedtissue section comprising the steps of a) providing a membrane slidecoated with poly-L-lysine, b) mounting the formalin-fixed,paraffin-embedded tissue section onto the membrane slide, c) removingthe paraffin from the formalin-fixed, paraffin-embedded tissue sectionby incubating the tissue section mounted on the solid support in xylol,d) heating the tissue section mounted on the membrane slide to retrieveepitopes at about 60° C. for about 16 h, and e) staining the tissuesection mounted on the membrane slide by use of a labeled antibody, f)microdissecting from the stained tissue section mounted on the membraneslide an area of interest having a size of 1-2 mm², g) isolating RNAfrom the area of interest, h) reverse transcribing the isolated RNA intocDNA, i) amplifying and quantifying the cDNA, wherein at least step e)is performed in the presence of about 2 M sodium chloride and whereinthe step of amplifying and quantifying the cDNA is performed by RealTime PCR.

The present description further refers to a kit for performing themethod as described above. Thus, the present description further refersto a kit for performing a method for immuno-histochemical staining of aformalin-fixed, paraffin-embedded tissue section comprising the steps ofa) providing a solid support, b) mounting the formalin-fixed,paraffin-embedded tissue section onto the solid support, c) removing theparaffin from the formalin-fixed, paraffin-embedded tissue section, d)heating the tissue section mounted on the solid support to retrieveepitopes at 50 to 70° C. for 12 to 24 h, and e) staining the tissuesection mounted on the solid support, wherein at least step e) isperformed in the presence of 0.5 to 3.0 M sodium chloride. In oneembodiment, the sodium chloride is present in a concentration of 1.5 to2.5 M. In a more specific embodiment, the sodium chloride is present ina concentration of about 1.8 to 2.2 M. In an even more specificembodiment, the sodium chloride is present in a concentration of about 2M.

In one embodiment, the method performed with the kit further comprisesthe steps of f) dissecting from the stained tissue section mounted onthe solid support an area of interest, g) isolating RNA from the area ofinterest, h) reverse transcribing the isolated RNA into cDNA, i)amplifying and quantifying the cDNA. In one embodiment, steps h) and i)are performed as one-step PCR. In another embodiment, steps h) and i)are performed as two-step PCR. In a specific embodiment, the step ofamplifying and quantifying the cDNA is performed by Real Time PCR.

In one embodiment, the kit for performing the method according to thedescription comprises a) a solid support, b) a solution for epitoperetrieval, and c) a solution for immuno-histochemical stainingcomprising sodium chloride in a concentration of 0.5 to 3.0 M. Inanother embodiment, the kit for performing the method according to thedescription comprises a) a membrane slide coated with poly-lysine, b) asolution for epitope retrieval, and c) a solution forimmuno-histochemical staining comprising sodium chloride in aconcentration of 0.5 to 3.0 M. In a specific embodiment the kit furthercomprises all reagents necessary for performing reverse transcriptionfrom RNA into cDNA, and amplification and quantitation of the cDNA. Inanother specific embodiment the kit comprises all reagents necessary forperforming reverse transcription from RNA into cDNA, preamplifying thecDNA, and amplifying and quantifying the preamplified cDNA.

The following examples 1-3 are provided to aid the understanding of thepresent invention, the true scope of which is set forth in the appendedclaims. It is understood that modifications can be made in theprocedures set forth without departing from the spirit of the invention.

Example 1 Coating of Membrane Slides with Poly-L-Lysine

The PEN membrane slides (MicroDissect GmbH) were covered with about 1 mlpoly-L-lysine solution (0.1% w/v, Sigma-Aldrich Chemie GmbH) andincubated for 30 min in a humidity chamber at room temperature. Thepoly-L-lysine solution was removed by performing powerful shaking.Subsequently the PEN membrane slides were dried overnight underUV-Light.

Observed Results (not Shown):

Coating of the PEN membrane slides with poly-L-lysine lead to anincreased attachment of the tissue section to the membrane slide whenapplied to low-temperature heat induced epitope retrieval (LT-HIER, 60°C. 16 h, pH 8). Membrane slides coated with poly-L-lysine: 0 of 3 tissuesections detached from the slide. Membrane slides without poly-L-lysine:3 of 3 tissue sections detached from the slide.

Example 2 CD31-Staining without/with 2 M Sodium Chloride

FFPET sections of tumor samples were used for antibody-based stainingand subsequent RNA isolation. The following description only refers tothe procedure performed to stain the FFPET sections in presence of 2 Msodium chloride. For experiments without sodium chloride, exactly thesame procedure was performed with the following differences: 1) Sodiumchloride was omitted in the staining procedure, 2) the incubation withthe secondary antibody was performed for 30 min (instead of 2 h with 2 Msodium chloride). The high salt concentration required an increasedincubation time due to reduced binding efficiency of the secondaryantibody.

5 μm FFPET sections were attached on poly-L-Lysine-coated PEN membraneslides and dried overnight in dust free environment. Subsequently, theFFPET sections were incubated for 5 min in 3% H₂O₂ (AppliChem GmbH).Then the FFPET sections were washed 2 min in H₂O PCR-Grade. Incubationof the sections was performed for 16 h at 60° C. in Epitope RetrievalSolution (Leica Microsystems GmbH). Afterwards, CD31-staining withEnVision™ anti-Mouse (DAKO GmbH) was performed. Sodium chloride(molecular biology grade, Sigma-Aldrich Chemie GmbH) was dissolved inall staining reagents (Protein Block serum free (DAKO GmbH), primary andsecondary antibody, DAB-Chromogen (Thermo Fisher Scientific GmbH) andTris-Buffered Saline and Tween 20 (TBS-T) wash buffer). The finalconcentration of sodium chloride was about 2 M. The sections were cooledto room temperature for 5 min in TBS-T/sodium chloride. Sections wereincubated with 100 μl protein block/sodium chloride for 5 min in thehumidity chamber. Subsequently, the liquid was shaken off the sectionsand 100 μl primary antibody/sodium chloride was added, covered withparafilm and incubated 1 h at 37° C. The sections were washed 2×2 minwith TBS-T/sodium chloride and afterwards 100 μl secondaryantibody/sodium chloride was added and incubated 2 h at room temperaturein the humidity chamber. After washing 2×2 min with TBS-T/sodiumchloride, 100 μl OF DAB-Chromogen/sodium chloride was added andincubated 5-10 min at room temperature in the humidity chamber. Thesections were washed 2 min with TBS-T/sodium chloride. Subsequently, thesections were washed 2 min with H₂O (PCR-Grade). The stained sectionswere dissected and total RNA was isolated (High Pure Paraffin RNA Kit,Roche Diagnostics GmbH). RNA concentration was determined by spectralphotometric analysis (NanoDrop ND 1000 Spectralphotometer). RNA wastranscribed into cDNA by the methods well known in the art cDNA waspre-amplified. Subsequently, amplification was performed by real-timePCR (LightCycler® Platform).

Observed Results:

The RNA-concentrations of the CD31-stained sections without sodiumchloride are significantly lower as compared to the unstained sections.The RNA concentrations of the CD31-stained FFPET sections with sodiumchloride do not differ significantly from the unstained sections (seeFIG. 1).

The Cp-values (reference gene HPRT) of the CD31-stained sections withoutsodium chloride are significantly higher as compared to the unstainedsections. The Cp-Values of the CD31-stained FFPET sections with sodiumchloride do not differ significantly from the unstained sections (seeFIG. 2).

The Cp-values (reference gene ALAS1) of the CD31-stained sectionswithout sodium chloride are significantly higher as compared to theunstained sections. The Cp-Values of the CD31-stained FFPE sections withsodium chloride do not differ significantly from the unstained sections(see FIG. 3).

Example 3 Gene Expression Analysis of Two Markers from CD31-StainedFFPET Sections

The example shows the suitability of RNA isolated from CD-31-stainedFFPET sections with the method according to the description for geneexpression experiments. The method described in Example 2 was applied toFFPET sections from three independent tumor samples. The samples weremounted on membrane slides. Areas of interest (tumor and vessels) weremicrodissected using successive laser capture microdissection. Data onthe expression of two different markers (Marker 1 and Marker 2) in tumordissections and vessel dissections, respectively, were obtained byanalyzing the isolated RNA. Experiments were performed in duplicates.The RNA was transcribed into cDNA using methods well known in the art.The cDNA was pre-amplified to obtain sufficient starting material and toincrease sensitivity. The pre-amplified cDNA was finally analyzed induplicates using Real Time PCR. Relative expression of Marker 1 andMarker 2 was obtained by normalizing the expression of Marker 1 andMarker 2 to the reference gene HPRT, respectively.

Observed Results:

In consistence with previous experiments performed on unstained tumorsamples (data not shown), FIG. 4 shows data regarding the pattern of therelative expression of Marker 1 and Marker 2 obtained from threeindependent CD31-stained tumor samples. FIG. 4 A) shows that Marker 1 isexpressed to a larger extend in tumor cells as compared to vessel cells.Furthermore, FIG. 4 B) shows that Marker 2 is expressed to a largerextend in vessel cells as compared to tumor cells. In this case, theexpression in tumor cells is very low as compared to the vessel cellssuch that an expression cannot be detected (not detected=n.d.). As theanalysis of the unstained tumor samples (data not shown) could bereproduced, it can be concluded that the staining method according tothe description is not significantly influencing the RNA quality in away that the results are affected. Consequently, with the methodaccording to the description, RNA degradation can be minimized such thatthe quality of RNA from FFPET samples is sufficient for gene expressionanalysis or any other method for analyzing RNA.

1. A method for immuno-histochemical staining of a formalin-fixed,paraffin-embedded tissue section comprising the steps of: (a) providinga solid support, (b) mounting the formalin-fixed, paraffin-embeddedtissue section onto the solid support, (c) removing the paraffin fromthe formalin-fixed, paraffin-embedded tissue section, (d) heating thetissue section mounted on the solid support to retrieve epitopes at 50to 70° C. for 12 to 24 h, and (e) staining the tissue section mounted onthe solid support, wherein at least step e) is performed in the presenceof 0.5 to 3.0 M sodium chloride.
 2. The method of claim 1 furthercomprising the steps of: (f) dissecting from the stained tissue sectionmounted on the solid support an area of interest, (g) isolating RNA fromthe area of interest, (h) reverse transcribing the isolated RNA intocDNA, and (i) amplifying and quantifying the cDNA.
 3. The method ofclaim 1, wherein the solid support is coated with poly-L-lysine.
 4. Themethod of claim 1, wherein sodium chloride is present in a concentrationof 1.5 to 2.5 M.
 5. The method of claim 1, wherein sodium chloride ispresent in a concentration of about 2 M.
 6. The method of claim 1,wherein removing the paraffin is performed by incubating the tissuesection mounted on the solid support in xylol.
 7. The method of claim 1,wherein heating of the tissue section mounted on the solid support isperformed at 55 to 65° C. for 14 to 18 h.
 8. The method of claim 1,wherein heating of the tissue section mounted on the solid support isperformed at about 60° C. for about 16 h.
 9. The method of claim 1,wherein the staining comprises the use of a labeled antibody.
 10. Themethod of claim 1, wherein the solid support is a membrane slide. 11.The method of claim 2, wherein step f) comprises microdissecting ormacrodissecting the area of interest.
 12. The method of claim 2, whereinthe area of interest has a size of 1-2 mm².
 13. The method of claim 2,wherein the step of amplifying and quantifying the cDNA is performed byReal Time PCR.
 14. A kit comprising: (a) a solid support coated withpoly-lysine, (b) a solution for epitope retrieval, and (c) a solutionfor immuno-histochemical staining comprising sodium chloride in aconcentration of 0.5 to 3.0 M.
 15. The kit according to claim 14,wherein the kit further comprises all reagents necessary for performingreverse transcription from RNA into cDNA, amplification and quantitationof the cDNA.